#!/bin/bash
file_1=/raid/shubham/HARC/data/NA12878-Rep-1_S1_S2_R1.fastq
file_2=/raid/shubham/HARC/data/NA12878-Rep-1_S1_S2_R2.fastq
logname=logs/8_29_18/NA12878-Rep-1_S1_S2.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/NA12878-Rep-1_S1_L001_R1_001.fastq
file_2=/raid/shubham/HARC/data/NA12878-Rep-1_S1_L001_R2_001.fastq
logname=logs/8_29_18/NA12878-Rep-1_S1_L001.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/SRR554369_1.fastq
file_2=/raid/shubham/HARC/data/SRR554369_2.fastq
logname=logs/8_29_18/SRR554369.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/SRR327342_1.fastq
file_2=/raid/shubham/HARC/data/SRR327342_2.fastq
logname=logs/8_29_18/SRR327342.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/ERR532393_1.fastq
file_2=/raid/shubham/HARC/data/ERR532393_2.fastq
logname=logs/8_29_18/ERR532393.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/SRR870667_2.fastq
logname=logs/8_29_18/SRR870667_2.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/NA12878-Rep-1_S1_S2_R1.fastq.trimmed
file_2=/raid/shubham/HARC/data/NA12878-Rep-1_S1_S2_R2.fastq.trimmed
logname=logs/8_29_18/NA12878-Rep-1_S1_S2.trimmed.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/NA12878-Rep-1_S1_L001_R1_001.fastq.trimmed
file_2=/raid/shubham/HARC/data/NA12878-Rep-1_S1_L001_R2_001.fastq.trimmed
logname=logs/8_29_18/NA12878-Rep-1_S1_L001.trimmed.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/HS_28_1.fastq
file_2=/raid/shubham/HARC/data/HS_28_2.fastq
logname=logs/8_29_18/HS_28.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/SRR1770413_1.fastq
file_2=/raid/shubham/HARC/data/SRR1770413_2.fastq
logname=logs/8_29_18/SRR1770413.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/SRR062634_1.fastq
file_2=/raid/shubham/HARC/data/SRR062634_2.fastq
logname=logs/8_29_18/SRR062634.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"

file_1=/raid/shubham/HARC/data/PhiX_100M_1.fastq
file_2=/raid/shubham/HARC/data/PhiX_100M_2.fastq
logname=logs/8_29_18/PhiX_100M.log
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_1 $file_1".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc c -t8 -v $file_2 $file_2".dsrc" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_1".dsrc" $file_1".d" |& tee -a $logname
stdbuf -oL /usr/bin/time -v ./../DSRC/bin/dsrc d -t8 -v $file_2".dsrc" $file_2".d" |& tee -a $logname
rm $file_1".d" $file_2".d"
